MDS analysis

Goal: count SNP difference between LTR and LTNR on a per gene basis

library(tidyverse)

── Attaching packages ───────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ──────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(ggrepel)

get the vcf header

vcf.header <- system("zgrep '#C' ../input/LT.vcf.gz",intern = TRUE) 
vcf.header

[1] "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t38LTR\t42LTR\t42LTRR\t43LTR\t43LTRR\t49LTWR\t49LTWRR\t95LTWR\t95LTWRR\t99LTWR"

vcf.header <- vcf.header %>% 
  str_replace("#","") %>% #get rid of the pound sign
  str_split(pattern = "\t") %>% #split on the tabs
  magrittr::extract2(1)
vcf.header

 [1] "CHROM"   "POS"     "ID"      "REF"     "ALT"     "QUAL"    "FILTER"  "INFO"    "FORMAT" 
[10] "38LTR"   "42LTR"   "42LTRR"  "43LTR"   "43LTRR"  "49LTWR"  "49LTWRR" "95LTWR"  "95LTWRR"
[19] "99LTWR" 

get the data

snps <- read_tsv("../input/LT.vcf.gz", na = c("","NA","."),comment="#",col_names = vcf.header) %>%
  select(-ID, -FILTER) # these are empty columns

Parsed with column specification:
cols(
  CHROM = col_character(),
  POS = col_integer(),
  ID = col_character(),
  REF = col_character(),
  ALT = col_character(),
  QUAL = col_double(),
  FILTER = col_character(),
  INFO = col_character(),
  FORMAT = col_character(),
  `38LTR` = col_character(),
  `42LTR` = col_character(),
  `42LTRR` = col_character(),
  `43LTR` = col_character(),
  `43LTRR` = col_character(),
  `49LTWR` = col_character(),
  `49LTWRR` = col_character(),
  `95LTWR` = col_character(),
  `95LTWRR` = col_character(),
  `99LTWR` = col_character()
)

|=======                                                                       |   9%   36 MB
|=======                                                                       |   9%   36 MB
|=======                                                                       |   9%   37 MB
|=======                                                                       |   9%   37 MB
|=======                                                                       |   9%   37 MB
|=======                                                                       |   9%   38 MB
|=======                                                                       |   9%   38 MB
|=======                                                                       |   9%   39 MB
|=======                                                                       |   9%   39 MB
|=======                                                                       |   9%   39 MB
|=======                                                                       |  10%   40 MB
|========                                                                      |  10%   40 MB
|========                                                                      |  10%   40 MB
|========                                                                      |  10%   41 MB
|========                                                                      |  10%   41 MB
|========                                                                      |  10%   42 MB
|========                                                                      |  10%   42 MB
|========                                                                      |  10%   42 MB
|========                                                                      |  10%   43 MB
|========                                                                      |  10%   43 MB
|========                                                                      |  11%   44 MB
|========                                                                      |  11%   44 MB
|========                                                                      |  11%   44 MB
|========                                                                      |  11%   45 MB
|=========                                                                     |  11%   45 MB
|=========                                                                     |  11%   46 MB
|=========                                                                     |  11%   46 MB
|=========                                                                     |  11%   46 MB
|=========                                                                     |  11%   47 MB
|=========                                                                     |  11%   47 MB
|=========                                                                     |  12%   47 MB
|=========                                                                     |  12%   48 MB
|=========                                                                     |  12%   48 MB
|=========                                                                     |  12%   49 MB
|=========                                                                     |  12%   49 MB
|=========                                                                     |  12%   49 MB
|=========                                                                     |  12%   50 MB
|==========                                                                    |  12%   50 MB
|==========                                                                    |  12%   51 MB
|==========                                                                    |  12%   51 MB
|==========                                                                    |  12%   51 MB
|==========                                                                    |  13%   52 MB
|==========                                                                    |  13%   52 MB
|==========                                                                    |  13%   53 MB
|==========                                                                    |  13%   53 MB
|==========                                                                    |  13%   53 MB
|==========                                                                    |  13%   54 MB
|==========                                                                    |  13%   54 MB
|==========                                                                    |  13%   54 MB
|==========                                                                    |  13%   55 MB
|===========                                                                   |  13%   55 MB
|===========                                                                   |  14%   56 MB
|===========                                                                   |  14%   56 MB
|===========                                                                   |  14%   56 MB
|===========                                                                   |  14%   57 MB
|===========                                                                   |  14%   57 MB
|===========                                                                   |  14%   57 MB
|===========                                                                   |  14%   58 MB
|===========                                                                   |  14%   58 MB
|===========                                                                   |  14%   59 MB
|===========                                                                   |  14%   59 MB
|===========                                                                   |  15%   59 MB
|===========                                                                   |  15%   60 MB
|============                                                                  |  15%   60 MB
|============                                                                  |  15%   61 MB
|============                                                                  |  15%   61 MB
|============                                                                  |  15%   61 MB
|============                                                                  |  15%   62 MB
|============                                                                  |  15%   62 MB
|============                                                                  |  15%   63 MB
|============                                                                  |  15%   63 MB
|============                                                                  |  15%   63 MB
|============                                                                  |  16%   64 MB
|============                                                                  |  16%   64 MB
|============                                                                  |  16%   64 MB
|============                                                                  |  16%   65 MB
|=============                                                                 |  16%   65 MB
|=============                                                                 |  16%   66 MB
|=============                                                                 |  16%   66 MB
|=============                                                                 |  16%   66 MB
|=============                                                                 |  16%   67 MB
|=============                                                                 |  16%   67 MB
|=============                                                                 |  17%   68 MB
|=============                                                                 |  17%   68 MB
|=============                                                                 |  17%   68 MB
|=============                                                                 |  17%   69 MB
|=============                                                                 |  17%   69 MB
|=============                                                                 |  17%   69 MB
|=============                                                                 |  17%   70 MB
|==============                                                                |  17%   70 MB
|==============                                                                |  17%   71 MB
|==============                                                                |  17%   71 MB
|==============                                                                |  18%   71 MB
|==============                                                                |  18%   72 MB
|==============                                                                |  18%   72 MB
|==============                                                                |  18%   73 MB
|==============                                                                |  18%   73 MB
|==============                                                                |  18%   73 MB
|==============                                                                |  18%   74 MB
|==============                                                                |  18%   74 MB
|==============                                                                |  18%   74 MB
|==============                                                                |  18%   75 MB
|==============                                                                |  18%   75 MB
|===============                                                               |  19%   76 MB
|===============                                                               |  19%   76 MB
|===============                                                               |  19%   76 MB
|===============                                                               |  19%   77 MB
|===============                                                               |  19%   77 MB
|===============                                                               |  19%   78 MB
|===============                                                               |  19%   78 MB
|===============                                                               |  19%   78 MB
|===============                                                               |  19%   79 MB
|===============                                                               |  19%   79 MB
|===============                                                               |  20%   79 MB
|===============                                                               |  20%   80 MB
|===============                                                               |  20%   80 MB
|================                                                              |  20%   81 MB
|================                                                              |  20%   81 MB
|================                                                              |  20%   81 MB
|================                                                              |  20%   82 MB
|================                                                              |  20%   82 MB
|================                                                              |  20%   83 MB
|================                                                              |  20%   83 MB
|================                                                              |  21%   83 MB
|================                                                              |  21%   84 MB
|================                                                              |  21%   84 MB
|================                                                              |  21%   84 MB
|================                                                              |  21%   85 MB
|================                                                              |  21%   85 MB
|=================                                                             |  21%   86 MB
|=================                                                             |  21%   86 MB
|=================                                                             |  21%   86 MB
|=================                                                             |  21%   87 MB
|=================                                                             |  21%   87 MB
|=================                                                             |  22%   87 MB
|=================                                                             |  22%   88 MB
|=================                                                             |  22%   88 MB
|=================                                                             |  22%   89 MB
|=================                                                             |  22%   89 MB
|=================                                                             |  22%   89 MB
|=================                                                             |  22%   90 MB
|=================                                                             |  22%   90 MB
|==================                                                            |  22%   91 MB
|==================                                                            |  22%   91 MB
|==================                                                            |  23%   91 MB
|==================                                                            |  23%   92 MB
|==================                                                            |  23%   92 MB
|==================                                                            |  23%   92 MB
|==================                                                            |  23%   93 MB
|==================                                                            |  23%   93 MB
|==================                                                            |  23%   94 MB
|==================                                                            |  23%   94 MB
|==================                                                            |  23%   94 MB
|==================                                                            |  23%   95 MB
|==================                                                            |  23%   95 MB
|===================                                                           |  24%   95 MB
|===================                                                           |  24%   96 MB
|===================                                                           |  24%   96 MB
|===================                                                           |  24%   97 MB
|===================                                                           |  24%   97 MB
|===================                                                           |  24%   97 MB
|===================                                                           |  24%   98 MB
|===================                                                           |  24%   98 MB
|===================                                                           |  24%   99 MB
|===================                                                           |  24%   99 MB
|===================                                                           |  25%   99 MB
|===================                                                           |  25%  100 MB
|===================                                                           |  25%  100 MB
|===================                                                           |  25%  100 MB
|====================                                                          |  25%  101 MB
|====================                                                          |  25%  101 MB
|====================                                                          |  25%  102 MB
|====================                                                          |  25%  102 MB
|====================                                                          |  25%  102 MB
|====================                                                          |  25%  103 MB
|====================                                                          |  25%  103 MB
|====================                                                          |  26%  104 MB
|====================                                                          |  26%  104 MB
|====================                                                          |  26%  104 MB
|====================                                                          |  26%  105 MB
|====================                                                          |  26%  105 MB
|====================                                                          |  26%  105 MB
|=====================                                                         |  26%  106 MB
|=====================                                                         |  26%  106 MB
|=====================                                                         |  26%  107 MB
|=====================                                                         |  26%  107 MB
|=====================                                                         |  27%  107 MB
|=====================                                                         |  27%  108 MB
|=====================                                                         |  27%  108 MB
|=====================                                                         |  27%  109 MB
|=====================                                                         |  27%  109 MB
|=====================                                                         |  27%  109 MB
|=====================                                                         |  27%  110 MB
|=====================                                                         |  27%  110 MB
|=====================                                                         |  27%  110 MB
|======================                                                        |  27%  111 MB
|======================                                                        |  27%  111 MB
|======================                                                        |  28%  112 MB
|======================                                                        |  28%  112 MB
|======================                                                        |  28%  112 MB
|======================                                                        |  28%  113 MB
|======================                                                        |  28%  113 MB
|======================                                                        |  28%  114 MB
|======================                                                        |  28%  114 MB
|======================                                                        |  28%  114 MB
|======================                                                        |  28%  115 MB
|======================                                                        |  28%  115 MB
|======================                                                        |  29%  116 MB
|=======================                                                       |  29%  116 MB
|=======================                                                       |  29%  116 MB
|=======================                                                       |  29%  117 MB
|=======================                                                       |  29%  117 MB
|=======================                                                       |  29%  117 MB
|=======================                                                       |  29%  118 MB
|=======================                                                       |  29%  118 MB
|=======================                                                       |  29%  119 MB
|=======================                                                       |  29%  119 MB
|=======================                                                       |  30%  119 MB
|=======================                                                       |  30%  120 MB
|=======================                                                       |  30%  120 MB
|=======================                                                       |  30%  121 MB
|========================                                                      |  30%  121 MB
|========================                                                      |  30%  121 MB
|========================                                                      |  30%  122 MB
|========================                                                      |  30%  122 MB
|========================                                                      |  30%  122 MB
|========================                                                      |  30%  123 MB
|========================                                                      |  31%  123 MB
|========================                                                      |  31%  124 MB
|========================                                                      |  31%  124 MB
|========================                                                      |  31%  124 MB
|========================                                                      |  31%  125 MB
|========================                                                      |  31%  125 MB
|========================                                                      |  31%  126 MB
|=========================                                                     |  31%  126 MB
|=========================                                                     |  31%  126 MB
|=========================                                                     |  31%  127 MB
|=========================                                                     |  31%  127 MB
|=========================                                                     |  32%  128 MB
|=========================                                                     |  32%  128 MB
|=========================                                                     |  32%  128 MB
|=========================                                                     |  32%  129 MB
|=========================                                                     |  32%  129 MB
|=========================                                                     |  32%  129 MB
|=========================                                                     |  32%  130 MB
|=========================                                                     |  32%  130 MB
|=========================                                                     |  32%  131 MB
|==========================                                                    |  32%  131 MB
|==========================                                                    |  33%  131 MB
|==========================                                                    |  33%  132 MB
|==========================                                                    |  33%  132 MB
|==========================                                                    |  33%  133 MB
|==========================                                                    |  33%  133 MB
|==========================                                                    |  33%  133 MB
|==========================                                                    |  33%  134 MB
|==========================                                                    |  33%  134 MB
|==========================                                                    |  33%  135 MB
|==========================                                                    |  33%  135 MB
|==========================                                                    |  34%  135 MB
|==========================                                                    |  34%  136 MB
|===========================                                                   |  34%  136 MB
|===========================                                                   |  34%  137 MB
|===========================                                                   |  34%  137 MB
|===========================                                                   |  34%  137 MB
|===========================                                                   |  34%  138 MB
|===========================                                                   |  34%  138 MB
|===========================                                                   |  34%  139 MB
|===========================                                                   |  34%  139 MB
|===========================                                                   |  35%  139 MB
|===========================                                                   |  35%  140 MB
|===========================                                                   |  35%  140 MB
|===========================                                                   |  35%  141 MB
|============================                                                  |  35%  141 MB
|============================                                                  |  35%  141 MB
|============================                                                  |  35%  142 MB
|============================                                                  |  35%  142 MB
|============================                                                  |  35%  142 MB
|============================                                                  |  35%  143 MB
|============================                                                  |  36%  143 MB
|============================                                                  |  36%  144 MB
|============================                                                  |  36%  144 MB
|============================                                                  |  36%  144 MB
|============================                                                  |  36%  145 MB
|============================                                                  |  36%  145 MB
|============================                                                  |  36%  146 MB
|=============================                                                 |  36%  146 MB
|=============================                                                 |  36%  146 MB
|=============================                                                 |  36%  147 MB
|=============================                                                 |  37%  147 MB
|=============================                                                 |  37%  148 MB
|=============================                                                 |  37%  148 MB
|=============================                                                 |  37%  148 MB
|=============================                                                 |  37%  149 MB
|=============================                                                 |  37%  149 MB
|=============================                                                 |  37%  150 MB
|=============================                                                 |  37%  150 MB
|=============================                                                 |  37%  150 MB
|=============================                                                 |  37%  151 MB
|==============================                                                |  37%  151 MB
|==============================                                                |  38%  151 MB
|==============================                                                |  38%  152 MB
|==============================                                                |  38%  152 MB
|==============================                                                |  38%  153 MB
|==============================                                                |  38%  153 MB
|==============================                                                |  38%  153 MB
|==============================                                                |  38%  154 MB
|==============================                                                |  38%  154 MB
|==============================                                                |  38%  155 MB
|==============================                                                |  38%  155 MB
|==============================                                                |  39%  155 MB
|==============================                                                |  39%  156 MB
|===============================                                               |  39%  156 MB
|===============================                                               |  39%  157 MB
|===============================                                               |  39%  157 MB
|===============================                                               |  39%  157 MB
|===============================                                               |  39%  158 MB
|===============================                                               |  39%  158 MB
|===============================                                               |  39%  159 MB
|===============================                                               |  39%  159 MB
|===============================                                               |  40%  159 MB
|===============================                                               |  40%  160 MB
|===============================                                               |  40%  160 MB
|===============================                                               |  40%  160 MB
|===============================                                               |  40%  161 MB
|================================                                              |  40%  161 MB
|================================                                              |  40%  162 MB
|================================                                              |  40%  162 MB
|================================                                              |  40%  162 MB
|================================                                              |  40%  163 MB
|================================                                              |  41%  163 MB
|================================                                              |  41%  164 MB
|================================                                              |  41%  164 MB
|================================                                              |  41%  164 MB
|================================                                              |  41%  165 MB
|================================                                              |  41%  165 MB
|================================                                              |  41%  166 MB
|================================                                              |  41%  166 MB
|=================================                                             |  41%  166 MB
|=================================                                             |  41%  167 MB
|=================================                                             |  42%  167 MB
|=================================                                             |  42%  168 MB
|=================================                                             |  42%  168 MB
|=================================                                             |  42%  168 MB
|=================================                                             |  42%  169 MB
|=================================                                             |  42%  169 MB
|=================================                                             |  42%  170 MB
|=================================                                             |  42%  170 MB
|=================================                                             |  42%  171 MB
|=================================                                             |  42%  171 MB
|==================================                                            |  43%  171 MB
|==================================                                            |  43%  172 MB
|==================================                                            |  43%  172 MB
|==================================                                            |  43%  173 MB
|==================================                                            |  43%  173 MB
|==================================                                            |  43%  173 MB
|==================================                                            |  43%  174 MB
|==================================                                            |  43%  174 MB
|==================================                                            |  43%  175 MB
|==================================                                            |  44%  175 MB
|==================================                                            |  44%  175 MB
|==================================                                            |  44%  176 MB
|===================================                                           |  44%  176 MB
|===================================                                           |  44%  177 MB
|===================================                                           |  44%  177 MB
|===================================                                           |  44%  177 MB
|===================================                                           |  44%  178 MB
|===================================                                           |  44%  178 MB
|===================================                                           |  44%  179 MB
|===================================                                           |  44%  179 MB
|===================================                                           |  45%  179 MB
|===================================                                           |  45%  180 MB
|===================================                                           |  45%  180 MB
|===================================                                           |  45%  181 MB
|===================================                                           |  45%  181 MB
|====================================                                          |  45%  181 MB
|====================================                                          |  45%  182 MB
|====================================                                          |  45%  182 MB
|====================================                                          |  45%  183 MB
|====================================                                          |  46%  183 MB
|====================================                                          |  46%  183 MB
|====================================                                          |  46%  184 MB
|====================================                                          |  46%  184 MB
|====================================                                          |  46%  185 MB
|====================================                                          |  46%  185 MB
|====================================                                          |  46%  185 MB
|====================================                                          |  46%  186 MB
|====================================                                          |  46%  186 MB
|=====================================                                         |  46%  187 MB
|=====================================                                         |  46%  187 MB
|=====================================                                         |  47%  187 MB
|=====================================                                         |  47%  188 MB
|=====================================                                         |  47%  188 MB
|=====================================                                         |  47%  188 MB
|=====================================                                         |  47%  189 MB
|=====================================                                         |  47%  189 MB
|=====================================                                         |  47%  190 MB
|=====================================                                         |  47%  190 MB
|=====================================                                         |  47%  190 MB
|=====================================                                         |  47%  191 MB
|=====================================                                         |  48%  191 MB
|======================================                                        |  48%  192 MB
|======================================                                        |  48%  192 MB
|======================================                                        |  48%  193 MB
|======================================                                        |  48%  193 MB
|======================================                                        |  48%  193 MB
|======================================                                        |  48%  194 MB
|======================================                                        |  48%  194 MB
|======================================                                        |  48%  194 MB
|======================================                                        |  48%  195 MB
|======================================                                        |  49%  195 MB
|======================================                                        |  49%  196 MB
|======================================                                        |  49%  196 MB
|======================================                                        |  49%  196 MB
|=======================================                                       |  49%  197 MB
|=======================================                                       |  49%  197 MB
|=======================================                                       |  49%  198 MB
|=======================================                                       |  49%  198 MB
|=======================================                                       |  49%  199 MB
|=======================================                                       |  49%  199 MB
|=======================================                                       |  50%  199 MB
|=======================================                                       |  50%  200 MB
|=======================================                                       |  50%  200 MB
|=======================================                                       |  50%  201 MB
|=======================================                                       |  50%  201 MB
|=======================================                                       |  50%  201 MB
|========================================                                      |  50%  202 MB
|========================================                                      |  50%  202 MB
|========================================                                      |  50%  203 MB
|========================================                                      |  50%  203 MB
|========================================                                      |  51%  203 MB
|========================================                                      |  51%  204 MB
|========================================                                      |  51%  204 MB
|========================================                                      |  51%  204 MB
|========================================                                      |  51%  205 MB
|========================================                                      |  51%  205 MB
|========================================                                      |  51%  206 MB
|========================================                                      |  51%  206 MB
|========================================                                      |  51%  206 MB
|=========================================                                     |  51%  207 MB
|=========================================                                     |  52%  207 MB
|=========================================                                     |  52%  208 MB
|=========================================                                     |  52%  208 MB
|=========================================                                     |  52%  208 MB
|=========================================                                     |  52%  209 MB
|=========================================                                     |  52%  209 MB
|=========================================                                     |  52%  210 MB
|=========================================                                     |  52%  210 MB
|=========================================                                     |  52%  210 MB
|=========================================                                     |  52%  211 MB
|=========================================                                     |  53%  211 MB
|=========================================                                     |  53%  212 MB
|==========================================                                    |  53%  212 MB
|==========================================                                    |  53%  212 MB
|==========================================                                    |  53%  213 MB
|==========================================                                    |  53%  213 MB
|==========================================                                    |  53%  213 MB
|==========================================                                    |  53%  214 MB
|==========================================                                    |  53%  214 MB
|==========================================                                    |  53%  215 MB
|==========================================                                    |  54%  215 MB
|==========================================                                    |  54%  216 MB
|==========================================                                    |  54%  216 MB
|==========================================                                    |  54%  216 MB
|===========================================                                   |  54%  217 MB
|===========================================                                   |  54%  217 MB
|===========================================                                   |  54%  217 MB
|===========================================                                   |  54%  218 MB
|===========================================                                   |  54%  218 MB
|===========================================                                   |  54%  219 MB
|===========================================                                   |  55%  219 MB
|===========================================                                   |  55%  219 MB
|===========================================                                   |  55%  220 MB
|===========================================                                   |  55%  220 MB
|===========================================                                   |  55%  221 MB
|===========================================                                   |  55%  221 MB
|===========================================                                   |  55%  221 MB
|============================================                                  |  55%  222 MB
|============================================                                  |  55%  222 MB
|============================================                                  |  55%  223 MB
|============================================                                  |  55%  223 MB
|============================================                                  |  56%  223 MB
|============================================                                  |  56%  224 MB
|============================================                                  |  56%  224 MB
|============================================                                  |  56%  224 MB
|============================================                                  |  56%  225 MB
|============================================                                  |  56%  225 MB
|============================================                                  |  56%  226 MB
|============================================                                  |  56%  226 MB
|============================================                                  |  56%  226 MB
|=============================================                                 |  56%  227 MB
|=============================================                                 |  57%  227 MB
|=============================================                                 |  57%  228 MB
|=============================================                                 |  57%  228 MB
|=============================================                                 |  57%  228 MB
|=============================================                                 |  57%  229 MB
|=============================================                                 |  57%  229 MB
|=============================================                                 |  57%  230 MB
|=============================================                                 |  57%  230 MB
|=============================================                                 |  57%  230 MB
|=============================================                                 |  57%  231 MB
|=============================================                                 |  58%  231 MB
|=============================================                                 |  58%  232 MB
|==============================================                                |  58%  232 MB
|==============================================                                |  58%  232 MB
|==============================================                                |  58%  233 MB
|==============================================                                |  58%  233 MB
|==============================================                                |  58%  233 MB
|==============================================                                |  58%  234 MB
|==============================================                                |  58%  234 MB
|==============================================                                |  58%  235 MB
|==============================================                                |  59%  235 MB
|==============================================                                |  59%  235 MB
|==============================================                                |  59%  236 MB
|==============================================                                |  59%  236 MB
|==============================================                                |  59%  237 MB
|===============================================                               |  59%  237 MB
|===============================================                               |  59%  237 MB
|===============================================                               |  59%  238 MB
|===============================================                               |  59%  238 MB
|===============================================                               |  59%  238 MB
|===============================================                               |  59%  239 MB
|===============================================                               |  60%  239 MB
|===============================================                               |  60%  240 MB
|===============================================                               |  60%  240 MB
|===============================================                               |  60%  240 MB
|===============================================                               |  60%  241 MB
|===============================================                               |  60%  241 MB
|===============================================                               |  60%  242 MB
|================================================                              |  60%  242 MB
|================================================                              |  60%  242 MB
|================================================                              |  60%  243 MB
|================================================                              |  61%  243 MB
|================================================                              |  61%  244 MB
|================================================                              |  61%  244 MB
|================================================                              |  61%  244 MB
|================================================                              |  61%  245 MB
|================================================                              |  61%  245 MB
|================================================                              |  61%  246 MB
|================================================                              |  61%  246 MB
|================================================                              |  61%  246 MB
|================================================                              |  61%  247 MB
|=================================================                             |  62%  247 MB
|=================================================                             |  62%  248 MB
|=================================================                             |  62%  248 MB
|=================================================                             |  62%  248 MB
|=================================================                             |  62%  249 MB
|=================================================                             |  62%  249 MB
|=================================================                             |  62%  249 MB
|=================================================                             |  62%  250 MB
|=================================================                             |  62%  250 MB
|=================================================                             |  62%  251 MB
|=================================================                             |  63%  251 MB
|=================================================                             |  63%  251 MB
|=================================================                             |  63%  252 MB
|==================================================                            |  63%  252 MB
|==================================================                            |  63%  253 MB
|==================================================                            |  63%  253 MB
|==================================================                            |  63%  253 MB
|==================================================                            |  63%  254 MB
|==================================================                            |  63%  254 MB
|==================================================                            |  63%  255 MB
|==================================================                            |  64%  255 MB
|==================================================                            |  64%  255 MB
|==================================================                            |  64%  256 MB
|==================================================                            |  64%  256 MB
|==================================================                            |  64%  256 MB
|==================================================                            |  64%  257 MB
|===================================================                           |  64%  257 MB
|===================================================                           |  64%  258 MB
|===================================================                           |  64%  258 MB
|===================================================                           |  64%  258 MB
|===================================================                           |  64%  259 MB
|===================================================                           |  65%  259 MB
|===================================================                           |  65%  260 MB
|===================================================                           |  65%  260 MB
|===================================================                           |  65%  260 MB
|===================================================                           |  65%  261 MB
|===================================================                           |  65%  261 MB
|===================================================                           |  65%  262 MB
|===================================================                           |  65%  262 MB
|====================================================                          |  65%  262 MB
|====================================================                          |  65%  263 MB
|====================================================                          |  66%  263 MB
|====================================================                          |  66%  264 MB
|====================================================                          |  66%  264 MB
|====================================================                          |  66%  264 MB
|====================================================                          |  66%  265 MB
|====================================================                          |  66%  265 MB
|====================================================                          |  66%  265 MB
|====================================================                          |  66%  266 MB
|====================================================                          |  66%  266 MB
|====================================================                          |  66%  267 MB
|====================================================                          |  67%  267 MB
|=====================================================                         |  67%  267 MB
|=====================================================                         |  67%  268 MB
|=====================================================                         |  67%  268 MB
|=====================================================                         |  67%  269 MB
|=====================================================                         |  67%  269 MB
|=====================================================                         |  67%  269 MB
|=====================================================                         |  67%  270 MB
|=====================================================                         |  67%  270 MB
|=====================================================                         |  67%  271 MB
|=====================================================                         |  68%  271 MB
|=====================================================                         |  68%  271 MB
|=====================================================                         |  68%  272 MB
|=====================================================                         |  68%  272 MB
|======================================================                        |  68%  273 MB
|======================================================                        |  68%  273 MB
|======================================================                        |  68%  273 MB
|======================================================                        |  68%  274 MB
|======================================================                        |  68%  274 MB
|======================================================                        |  68%  274 MB
|======================================================                        |  69%  275 MB
|======================================================                        |  69%  275 MB
|======================================================                        |  69%  276 MB
|======================================================                        |  69%  276 MB
|======================================================                        |  69%  277 MB
|======================================================                        |  69%  277 MB
|=======================================================                       |  69%  277 MB
|=======================================================                       |  69%  278 MB
|=======================================================                       |  69%  278 MB
|=======================================================                       |  69%  279 MB
|=======================================================                       |  70%  279 MB
|=======================================================                       |  70%  279 MB
|=======================================================                       |  70%  280 MB
|=======================================================                       |  70%  280 MB
|=======================================================                       |  70%  280 MB
|=======================================================                       |  70%  281 MB
|=======================================================                       |  70%  281 MB
|=======================================================                       |  70%  282 MB
|=======================================================                       |  70%  282 MB
|========================================================                      |  70%  282 MB
|========================================================                      |  71%  283 MB
|========================================================                      |  71%  283 MB
|========================================================                      |  71%  284 MB
|========================================================                      |  71%  284 MB
|========================================================                      |  71%  284 MB
|========================================================                      |  71%  285 MB
|========================================================                      |  71%  285 MB
|========================================================                      |  71%  285 MB
|========================================================                      |  71%  286 MB
|========================================================                      |  71%  286 MB
|========================================================                      |  71%  287 MB
|========================================================                      |  72%  287 MB
|=========================================================                     |  72%  287 MB
|=========================================================                     |  72%  288 MB
|=========================================================                     |  72%  288 MB
|=========================================================                     |  72%  289 MB
|=========================================================                     |  72%  289 MB
|=========================================================                     |  72%  289 MB
|=========================================================                     |  72%  290 MB
|=========================================================                     |  72%  290 MB
|=========================================================                     |  72%  290 MB
|=========================================================                     |  73%  291 MB
|=========================================================                     |  73%  291 MB
|=========================================================                     |  73%  292 MB
|=========================================================                     |  73%  292 MB
|=========================================================                     |  73%  292 MB
|==========================================================                    |  73%  293 MB
|==========================================================                    |  73%  293 MB
|==========================================================                    |  73%  294 MB
|==========================================================                    |  73%  294 MB
|==========================================================                    |  73%  294 MB
|==========================================================                    |  74%  295 MB
|==========================================================                    |  74%  295 MB
|==========================================================                    |  74%  296 MB
|==========================================================                    |  74%  296 MB
|==========================================================                    |  74%  296 MB
|==========================================================                    |  74%  297 MB
|==========================================================                    |  74%  297 MB
|===========================================================                   |  74%  298 MB
|===========================================================                   |  74%  298 MB
|===========================================================                   |  74%  298 MB
|===========================================================                   |  74%  299 MB
|===========================================================                   |  75%  299 MB
|===========================================================                   |  75%  299 MB
|===========================================================                   |  75%  300 MB
|===========================================================                   |  75%  300 MB
|===========================================================                   |  75%  301 MB
|===========================================================                   |  75%  301 MB
|===========================================================                   |  75%  301 MB
|===========================================================                   |  75%  302 MB
|===========================================================                   |  75%  302 MB
|===========================================================                   |  75%  303 MB
|============================================================                  |  76%  303 MB
|============================================================                  |  76%  303 MB
|============================================================                  |  76%  304 MB
|============================================================                  |  76%  304 MB
|============================================================                  |  76%  304 MB
|============================================================                  |  76%  305 MB
|============================================================                  |  76%  305 MB
|============================================================                  |  76%  306 MB
|============================================================                  |  76%  306 MB
|============================================================                  |  76%  306 MB
|============================================================                  |  77%  307 MB
|============================================================                  |  77%  307 MB
|============================================================                  |  77%  308 MB
|=============================================================                 |  77%  308 MB
|=============================================================                 |  77%  308 MB
|=============================================================                 |  77%  309 MB
|=============================================================                 |  77%  309 MB
|=============================================================                 |  77%  310 MB
|=============================================================                 |  77%  310 MB
|=============================================================                 |  77%  310 MB
|=============================================================                 |  78%  311 MB
|=============================================================                 |  78%  311 MB
|=============================================================                 |  78%  312 MB
|=============================================================                 |  78%  312 MB
|=============================================================                 |  78%  312 MB
|==============================================================                |  78%  313 MB
|==============================================================                |  78%  313 MB
|==============================================================                |  78%  313 MB
|==============================================================                |  78%  314 MB
|==============================================================                |  78%  314 MB
|==============================================================                |  78%  315 MB
|==============================================================                |  79%  315 MB
|==============================================================                |  79%  315 MB
|==============================================================                |  79%  316 MB
|==============================================================                |  79%  316 MB
|==============================================================                |  79%  317 MB
|==============================================================                |  79%  317 MB
|==============================================================                |  79%  317 MB
|===============================================================               |  79%  318 MB
|===============================================================               |  79%  318 MB
|===============================================================               |  79%  319 MB
|===============================================================               |  80%  319 MB
|===============================================================               |  80%  319 MB
|===============================================================               |  80%  320 MB
|===============================================================               |  80%  320 MB
|===============================================================               |  80%  320 MB
|===============================================================               |  80%  321 MB
|===============================================================               |  80%  321 MB
|===============================================================               |  80%  322 MB
|===============================================================               |  80%  322 MB
|===============================================================               |  80%  322 MB
|================================================================              |  81%  323 MB
|================================================================              |  81%  323 MB
|================================================================              |  81%  324 MB
|================================================================              |  81%  324 MB
|================================================================              |  81%  324 MB
|================================================================              |  81%  325 MB
|================================================================              |  81%  325 MB
|================================================================              |  81%  326 MB
|================================================================              |  81%  326 MB
|================================================================              |  81%  326 MB
|================================================================              |  82%  327 MB
|================================================================              |  82%  327 MB
|================================================================              |  82%  328 MB
|=================================================================             |  82%  328 MB
|=================================================================             |  82%  328 MB
|=================================================================             |  82%  329 MB
|=================================================================             |  82%  329 MB
|=================================================================             |  82%  330 MB
|=================================================================             |  82%  330 MB
|=================================================================             |  82%  330 MB
|=================================================================             |  83%  331 MB
|=================================================================             |  83%  331 MB
|=================================================================             |  83%  332 MB
|=================================================================             |  83%  332 MB
|=================================================================             |  83%  332 MB
|=================================================================             |  83%  333 MB
|==================================================================            |  83%  333 MB
|==================================================================            |  83%  333 MB
|==================================================================            |  83%  334 MB
|==================================================================            |  83%  334 MB
|==================================================================            |  83%  335 MB
|==================================================================            |  84%  335 MB
|==================================================================            |  84%  335 MB
|==================================================================            |  84%  336 MB
|==================================================================            |  84%  336 MB
|==================================================================            |  84%  337 MB
|==================================================================            |  84%  337 MB
|==================================================================            |  84%  337 MB
|==================================================================            |  84%  338 MB
|===================================================================           |  84%  338 MB
|===================================================================           |  84%  339 MB
|===================================================================           |  85%  339 MB
|===================================================================           |  85%  339 MB
|===================================================================           |  85%  340 MB
|===================================================================           |  85%  340 MB
|===================================================================           |  85%  341 MB
|===================================================================           |  85%  341 MB
|===================================================================           |  85%  341 MB
|===================================================================           |  85%  342 MB
|===================================================================           |  85%  342 MB
|===================================================================           |  85%  343 MB
|====================================================================          |  86%  343 MB
|====================================================================          |  86%  343 MB
|====================================================================          |  86%  344 MB
|====================================================================          |  86%  344 MB
|====================================================================          |  86%  345 MB
|====================================================================          |  86%  345 MB
|====================================================================          |  86%  345 MB
|====================================================================          |  86%  346 MB
|====================================================================          |  86%  346 MB
|====================================================================          |  86%  346 MB
|====================================================================          |  87%  347 MB
|====================================================================          |  87%  347 MB
|====================================================================          |  87%  348 MB
|====================================================================          |  87%  348 MB
|=====================================================================         |  87%  348 MB
|=====================================================================         |  87%  349 MB
|=====================================================================         |  87%  349 MB
|=====================================================================         |  87%  349 MB
|=====================================================================         |  87%  350 MB
|=====================================================================         |  87%  350 MB
|=====================================================================         |  88%  351 MB
|=====================================================================         |  88%  351 MB
|=====================================================================         |  88%  351 MB
|=====================================================================         |  88%  352 MB
|=====================================================================         |  88%  352 MB
|=====================================================================         |  88%  352 MB
|=====================================================================         |  88%  353 MB
|======================================================================        |  88%  353 MB
|======================================================================        |  88%  354 MB
|======================================================================        |  88%  354 MB
|======================================================================        |  88%  354 MB
|======================================================================        |  89%  355 MB
|======================================================================        |  89%  355 MB
|======================================================================        |  89%  355 MB
|======================================================================        |  89%  356 MB
|======================================================================        |  89%  356 MB
|======================================================================        |  89%  357 MB
|======================================================================        |  89%  357 MB
|======================================================================        |  89%  357 MB
|======================================================================        |  89%  358 MB
|======================================================================        |  89%  358 MB
|=======================================================================       |  89%  358 MB
|=======================================================================       |  90%  359 MB
|=======================================================================       |  90%  359 MB
|=======================================================================       |  90%  359 MB
|=======================================================================       |  90%  360 MB
|=======================================================================       |  90%  360 MB
|=======================================================================       |  90%  360 MB
|=======================================================================       |  90%  361 MB
|=======================================================================       |  90%  361 MB
|=======================================================================       |  90%  362 MB
|=======================================================================       |  90%  362 MB
|=======================================================================       |  90%  362 MB
|=======================================================================       |  91%  363 MB
|========================================================================      |  91%  363 MB
|========================================================================      |  91%  364 MB
|========================================================================      |  91%  364 MB
|========================================================================      |  91%  364 MB
|========================================================================      |  91%  365 MB
|========================================================================      |  91%  365 MB
|========================================================================      |  91%  366 MB
|========================================================================      |  91%  366 MB
|========================================================================      |  91%  366 MB
|========================================================================      |  92%  367 MB
|========================================================================      |  92%  367 MB
|========================================================================      |  92%  367 MB
|========================================================================      |  92%  368 MB
|=========================================================================     |  92%  368 MB
|=========================================================================     |  92%  369 MB
|=========================================================================     |  92%  369 MB
|=========================================================================     |  92%  369 MB
|=========================================================================     |  92%  370 MB
|=========================================================================     |  92%  370 MB
|=========================================================================     |  92%  370 MB
|=========================================================================     |  93%  371 MB
|=========================================================================     |  93%  371 MB
|=========================================================================     |  93%  372 MB
|=========================================================================     |  93%  372 MB
|=========================================================================     |  93%  372 MB
|=========================================================================     |  93%  373 MB
|=========================================================================     |  93%  373 MB
|==========================================================================    |  93%  373 MB
|==========================================================================    |  93%  374 MB
|==========================================================================    |  93%  374 MB
|==========================================================================    |  93%  374 MB
|==========================================================================    |  94%  375 MB
|==========================================================================    |  94%  375 MB
|==========================================================================    |  94%  375 MB
|==========================================================================    |  94%  376 MB
|==========================================================================    |  94%  376 MB
|==========================================================================    |  94%  377 MB
|==========================================================================    |  94%  377 MB
|==========================================================================    |  94%  377 MB
|==========================================================================    |  94%  378 MB
|==========================================================================    |  94%  378 MB
|===========================================================================   |  94%  378 MB
|===========================================================================   |  95%  379 MB
|===========================================================================   |  95%  379 MB
|===========================================================================   |  95%  379 MB
|===========================================================================   |  95%  380 MB
|===========================================================================   |  95%  380 MB
|===========================================================================   |  95%  380 MB
|===========================================================================   |  95%  381 MB
|===========================================================================   |  95%  381 MB
|===========================================================================   |  95%  382 MB
|===========================================================================   |  95%  382 MB
|===========================================================================   |  95%  382 MB
|===========================================================================   |  95%  383 MB
|===========================================================================   |  96%  383 MB
|===========================================================================   |  96%  383 MB
|============================================================================  |  96%  384 MB
|============================================================================  |  96%  384 MB
|============================================================================  |  96%  384 MB
|============================================================================  |  96%  385 MB
|============================================================================  |  96%  385 MB
|============================================================================  |  96%  385 MB
|============================================================================  |  96%  386 MB
|============================================================================  |  96%  386 MB
|============================================================================  |  96%  386 MB
|============================================================================  |  97%  387 MB
|============================================================================  |  97%  387 MB
|============================================================================  |  97%  387 MB
|============================================================================  |  97%  388 MB
|============================================================================  |  97%  388 MB
|============================================================================  |  97%  388 MB
|============================================================================= |  97%  389 MB
|============================================================================= |  97%  389 MB
|============================================================================= |  97%  389 MB
|============================================================================= |  97%  390 MB
|============================================================================= |  97%  390 MB
|============================================================================= |  97%  390 MB
|============================================================================= |  98%  391 MB
|============================================================================= |  98%  391 MB
|============================================================================= |  98%  391 MB
|============================================================================= |  98%  392 MB
|============================================================================= |  98%  392 MB
|============================================================================= |  98%  392 MB
|============================================================================= |  98%  393 MB
|============================================================================= |  98%  393 MB
|============================================================================= |  98%  393 MB
|==============================================================================|  98%  394 MB
|==============================================================================|  98%  394 MB
|==============================================================================|  98%  394 MB
|==============================================================================|  99%  395 MB
|==============================================================================|  99%  395 MB
|==============================================================================|  99%  395 MB
|==============================================================================|  99%  396 MB
|==============================================================================|  99%  396 MB
|==============================================================================|  99%  396 MB
|==============================================================================|  99%  397 MB
|==============================================================================|  99%  397 MB
|==============================================================================|  99%  397 MB
|==============================================================================|  99%  398 MB
|==============================================================================|  99%  398 MB
|==============================================================================|  99%  398 MB
|===============================================================================| 100%  398 MB

snps

filter to keep snps where there is data from all samples

snps <- snps %>% 
  filter({select(., matches("[0-9]")) %>% complete.cases() })
snps

snps <- snps %>% 
  mutate(TOTAL_DEPTH= {str_extract(INFO, "DP=[0-9]*") %>% 
      str_remove("DP=") %>%
      as.numeric() }
  ) %>%
  filter(QUAL >=100,
         nchar(ALT)==1,
         TOTAL_DEPTH > quantile(TOTAL_DEPTH, 0.05),
         TOTAL_DEPTH < quantile(TOTAL_DEPTH, 0.95))
snps

unpack the information differnet samples:

samples <- colnames(snps) %>% str_subset("^[0-9]")
for (s in samples) {
snps <- snps %>%
  separate(!!s, into=paste(s,c("gt","tot.depth","allele.depth","ref.depth","ref.qual","alt.depth","alt.qual","gt.lik"),sep="_"),
           sep=":", convert = TRUE)
}
snps

next steps

keep snps that are fixed differences between LTRR and LTNR

Count per gene

snps.l <- snps %>% select(CHROM, POS, ends_with("_gt")) %>%
  gather(key="plant", value="gt", -CHROM, -POS) %>%
  mutate(respnse=str_extract(plant, "LT[NR]{1,2}"))
snps.l